agriculture

Time to think outside the pot… oops, box! Apply for an APPF postgraduate internship award.

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The next round of Postgraduate Internship Awards at the Australian Plant Phenomics Facility (APPF) will close 30 November, 2017.

Internships are offered at the three APPF locations in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate? We can help!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required

PLUS

  • $10,000 maximum toward infrastructure use!

Multi-disciplinary opportunities

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

For more information and to apply click here.

Want to fly drones? New Remote Pilot Licence training course available

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Dr Ramesh Raja Segaran from APPF partner, URAF

The Unmanned Research Aircraft Facility (URAF) at the University of Adelaide, is offering a commercial drone course leading to the award of a Remote Pilot Licence (RePL) by the Civil Aviation Safety Authority of Australia (CASA).

This five-day intensive RePL course is conducted on University of Adelaide campuses by a team of CASA-certified drone operators and trainers from the University.

Course inclusions

  • All required theory and practical syllabus and requirements of CASA for a RePL.
  • Aeronautical Radio Operator Certificate (AROC).
  • English Language Proficiency certification (ELP).
  • Textbook: Remote Pilot Licence RePL Study Guide by Bob Tait and Ben Harris.
  • In-house examinations for ELP, AROC and RePL.

Assured quality teaching

Courses available

The URAF run regular RePL courses 4-6 times a year. Ad hoc RePL courses for government and industry groups are also available.

  • Remote Pilot Licence Course, Multi-rotor up to 7kg
    • $3500 + GST (includes textbook and application fees for RePL, AROC, ELP)
  • Practical type training for Multi-rotor/ Fixed wing up to 25kg
  • Others
    • If you have passed an aeronautical knowledge exam for a flight crew licence (e.g. PPL/ CPL), you can complete practical type training with the URAF to get type rated for a RePL.

Who needs a RePL?

Please contact the URAF for more information on the courses and how to enrol.

Decadal Plan for Australian Agricultural Sciences 2017-2026 released

Grow. Make. Prosper. The Decadal Plan for Australian Agricultural Sciences was published in June 2017 and presents the strategic vision for Australian Agricultural Sciences in the next decade.

The plan outlines strategies to improve the strength and efficiency of agricultural research in Australia in ways that will increase the ability of governments and producers to maintain productivity and efficiency in the face of evolving natural challenges. Successfully identifying, developing and deploying the next generation of game-changing scientific advances remains an active and ongoing challenge. The plan also outlines strategies to capitalise on emerging technologies that will affect the agricultural sciences.

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Agriculture is vitally important to Australia’s economy and social fabric, and contributes to global health and wellbeing. It faces a range of challenges across biophysical, economic and social arenas. Opportunities for technological and production improvements are continuously being identified from scientific research. However, to attain step change improvements in profitability, productivity and sustainability into the future will require integrated multidisciplinary research underpinned by a well-resourced science research pipeline.

The Australian Plant Phenomics Facility plays a key role in supporting the next generation of agricultural research designed to answer some of these challenges. This month we will meet with colleagues from fellow NCRIS facilities TERN, BPA, ALA, NeCTAR and NCI to explore opportunities for collaboration, determine where overlaps or synergies occur and discuss bigger picture ideas to ensure NCRIS funding is used most effectively.

Read the full Decadal Plan for Australian Agricultural Sciences (2017-2026) here.

Find out more about the APPF here.

National National Collaborative Research Infrastructure Strategy (NCRIS)

Terrestrial Ecosystem Research Network (TERN)

Bioplatforms Australia (BPA)

Australian Atlas of Living (ALA)

National eResearch Collaboration Tools and Resources (NeCTAR)

National Computational Infrastructure (NCI)

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An exciting offer of help for significant plant science research projects

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

This is an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)

 

 

Taking five with… Michael Schaefer

The three national nodes of the Australian Plant Phenomics Facility (APPF) are home to a highly talented team of plant science researchers and specialists. This passionate, cross-disciplinary team is skilled in areas such as agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics. But who are they?

Today we take five minutes to get to know…

Michael Schaefer, PhD

Tell us a little about where you work within the APPF.

I am based at the CSIRO node of the APPF in Canberra. This centre focuses on “deep phenotyping” (delving into metabolism and physiological processes within the plant) and “reverse phenomics” (dissecting traits to discover their mechanistic basis). Here, next generation research tools are being developed and applied to probe plant function and performance, under controlled conditions and in the field.

What do you do there?

I’m a Research Scientist and Team Leader of the Translational Phenomics and Services team. My team looks after all of the new projects that come into our node of the APPF, from dealing with clients directly, to designing experiments based on the client’s needs, right through to providing the final data products and support with analysis.

What is the best part of your job?

As one of the newest team members, the best part of my job has been meeting and working with new people and dealing with new projects in different plants and crops. Every case is different, so designing and running each project is unique which provides a lot of variety.

Where do you see plant phenomics research in 5-10 years time?

I think in 5-10 years’ time plant phenomics research will be very different. We can already see that sensors and technology are getting smaller, faster and cheaper. I think much of what we do with large sensors (lidar for example) will be replaced by much smaller handheld devices or drones that will process data on the fly and give you a result straight away. This will affect all areas of science, not just plant science, so I think it will just be something that we have to adjust to.

“The moment I realised I loved plant science was…”

Somewhere during my undergraduate degree. I was doing straight science, biology, chemistry and physics – very broad – and then I started making links with how physics could be related to the environment (i.e. plants etc.). This seemed to make more sense to me, as I could see the application and how it could directly affect people now, rather than working on something theoretical that may or may not ever be used.

If you could solve one plant science question, what would it be?

For me, I’m really interested in pastures, so it would be the holy grail to be able to accurately, remotely measure above-ground biomass and split it into the green and senesced fractions.

Pic of Michael Schaefer for blog

Michael Schaefer at the western entry of Angkor Wat, Cambodia

“When I am not working I am…”

At home spending time with my wife Ali and daughter Emilia, or outdoors playing cricket, golf or fishing.

If you could have one super power, what would it be?

Good question…. being able to bend time and space like Dr. Strange. That would be pretty cool!

“If I wasn’t a plant scientist I would be a…”

Fishing guide!

What is your most treasured possession?

They’re not a possession but my family are the most important to me.

If you could have dinner with two famous people who would they be?

Barack Obama and Tiger Woods.

What’s the one thing about you that would surprise people?

I have my private aeroplane pilot licence. I did my pilot training while I was doing my PhD – not that I get to fly much these days.

The APPF provides academic and commercial researchers with expert advice and access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field. We provide a suite of analytical tools to support high-throughput phenotyping and deep phenotyping in either controlled environments or in the field. Our dedicated team of experts provide consultation on project design and high quality customer support. If you would like to know more about our services and how we can support your plant science research, please contact us!

Taking the kinks out of curves

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

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An example of curve registration.  a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

 

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity.  The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Read the full paper, “Growth curve registration for evaluating salinity tolerance in barley” (DOI: 10.1186/s13007-017-0165-7) here.

Find out how the Australian Plant Phenomics Facility can support your plant science research here.

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High-throughput phenotyping in the Smarthouse™ at the Adelaide node of the APPF

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Barley plants growing in the Smarthouse™

 

 

Getting to the root of plant zinc health

Sunlight and water are two obvious requirements essential for healthy growth of plants, but did you know that zinc is also a vital ingredient? Zinc is a critical nutrient in hundreds of enzyme systems which are necessary for normal plant function. Zinc is also critical for human health – in fact, zinc is involved in more body functions than any other mineral.

Plants get zinc from the soil via their root systems. This uptake of nutrients is enhanced in many plants by mycorrhizal fungi which colonise the roots, creating a vast connection between the plant roots and the soil around them. Mycorrhizal fungi effectively increase the surface area of the roots, collecting nutrients from the soil beyond the reach of plant roots alone, and transfer these nutrients back to the plant.

Scientist, Dr Stephanie Watts-Williams, wants to find out how such mycorrhizal fungi can improve the zinc nutrition of plants, and subsequently impact on human health – particularly in countries where zinc malnutrition is a serious issue.

Read on here about Stephanie and her research at The Plant Accelerator®, Australian Plant Phenomics Facility, and other Waite Research Precinct partners.

Discover more about Stephanie’s research here or find her on Twitter:  @myco_research

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Dr Stephanie Watts-Williams at The Plant Accelerator®, Australian Plant Phenomics Facility